There are two species under the monograph of Radix Paeoniae Rubrae ("Chi-shao" in Chinese) in Chinese Pharmacopoeia 2005 edition-Paeonia lactiflora Pallas and Paeonia veitchii Lynch. Due to different species and growing conditions, there are significant chemical differences between the two species, which may result in the improper clinical usage under the same name. Chemical pattern expressed by high performance liquid chromatographic (HPLC) fingerprint analysis can play an important role in species differentiation and quality control of Radix Paeoniae Rubra. In the present work. HPLC fingerprints of two kinds of Radix Paeoniae Rubra have been established and analysed with chemometric methods including similarity evaluation and principal component analysis. Both of the fingerprint common patterns of the two species comprise 13 characteristic peaks, nine of which were common peaks of the two species. However, significant differences between the roots of R veitchii and P. lactiflora exist not only in the content of certain constituents, especially phenolic acids but also in peak-to-peak ratios expressed by the fingerprint patterns. According to the recent pharmacological studies on polyphenolic constituents, root originating from P. veitchii may possess better efficacy and quality than that from P. lactiflora. Our research reveals that further pharmacological investigation is very necessary to determine whether the two species should be embodied under the same monograph in Chinese Pharmacopoeia. (C) 2008 Elsevier B.V. All rights reserved.